Thermo Scientific Applied Biosystems QuantStudio 6 Pro Manuel utilisateur

For Research Use Only. Not for use in diagnostic procedures.

QuantStudio™6 Pro Real-Time PCR System

and QuantStudio™7 Pro Real-Time PCR

System

USER GUIDE

Publication Number MAN0018045

Revision G.0

Life Technologies Holdings Pte Ltd | Block 33 | Marsiling Industrial Estate Road 3 | #07-06, Singapore 739256

For descriptions of symbols on product labels or product documents, go to thermoﬁsher.com/symbols-deﬁnition.

The information in this guide is subject to change without notice.

DISCLAIMER: TO THE EXTENT ALLOWED BY LAW, THERMO FISHER SCIENTIFIC INC. AND/OR ITS AFFILIATE(S) WILL NOT BE

LIABLE FOR SPECIAL, INCIDENTAL, INDIRECT, PUNITIVE, MULTIPLE, OR CONSEQUENTIAL DAMAGES IN CONNECTION WITH OR

ARISING FROM THIS DOCUMENT, INCLUDING YOUR USE OF IT.

Revision history: Pub. No. MAN0018045

Revision Date Description

G.0 17 February 2021 v1.4.0

Updated centrifuges for the TaqMan™Array Card.

F.0 6 November 2020 v1.4.0

•Speciﬁed that the instrument and the desktop software must be connected to the same SAE server

for an account password to be updated on both applications.

•Provided the option of a static IP address or a dynamic IP address to connect to the SAE server.

•Corrected standards on 384-well RNase P plate (Figure 14 on page 105).

•Added a TaqMan™Array Card block, including system template ﬁle names, calibration workﬂow,

instructions to edit the plate ﬁle, and instructions to load and unload from the instrument

(QuantStudio™7 Pro System only).

•Added instructions to review the calibration status in the QuantStudio™Design and Analysis

Software v2.

•Added a peripheral self-test and updated the previous self-veriﬁcation test to a hardware test.

•Added instructions to upload a certiﬁcate for a TaqMan™Array Plate with RFID.

•Added the option of a voice recording for Smart Help.

•Added remote support.

•Updated the RFID labels (Figure 27 on page 215 and Figure 28 on page 216).

E.0 27 April 2020 v1.3.0

•Added protein thermal shift experiments to the instrument functions.

•Added a 96-well 0.1-mL block.

•Updated instructions to export data ﬁles when setting up a run and added instructions to import or

delete export settings.

•Updated instructions to save an edited run method.

•Updated instructions to add or edit reagents and then to apply the reagents to the plate.

•Updated instructions to view the ampliﬁcation plot after a run.

•Added instructions to view QC Check status after the run.

•Added information about a locked template ﬁle.

•Added functions for using the instrument with the SAE Administrator Console.

D.0 7 January 2020 v1.2.1

•Added information about position to set up facial authentication and to sign in with facial

authentication.

•Added instructions to test the connection to the Connect cloud-based platform and to view the

•Added instructions to repair the software after a software update.

•Changed port 7000 to 7443 for the instrument-to-computer connection.

•Corrected Ctto Cqin description of instrument veriﬁcation.

C.0 3 December 2019 v1.2.0

•Added a 384-well plate block.

•Updated instructions to set up facial authentication.

•Added a new voice command for calibration.

•Added custom melt curve run calibration.

Revision Date Description

C.0

(continued)

3 December 2019 •Added Security, Auditing, and E‑signature (SAE) v2.0 module.

•Added instructions to generate and reset an access key for external software to connect to the

instrument.

•Added instructions to import an Assay Information File.

•Corrected that a Connect proﬁle is required for the instrument schedule and Smart Help.

•Added new radio compliance standards.

B.0 22 August 2019 v1.1.0

•Corrected the text on the buttons for the following items:

–Add facial authentication to an existing instrument proﬁle.

–View the license agreement.

–Reset the instrument (restore factory default).

•Added the following items:

–TET™dye as a system dye.

–Information about sleep mode.

–Information about the automatic sign-out feature.

–The option to conﬁgure the instrument so that sign-in is required (guest access is not

permitted).

–Instructions to set up email notiﬁcation.

–Information about the speaker volume for each user.

–Instructions to back up the instrument and to restore a backup of the instrument.

–Information about multiple instruments and email notiﬁcation in the comparison of a local

instrument proﬁle and a Connect proﬁle.

–Instructions to unlink a Connect proﬁle.

–Instructions to update a PIN for a Connect proﬁle.

–Lighting guidelines for facial authentication.

–Radio compliance standards and RF transceiver speciﬁcations.

•Corrected the following items:

–Indicators for voice commands.

–Voice commands are only available in select countries.

–Instructions to remove VeriFlex™Zones and the Auto Delta setting.

–Excitation and emission wavelengths of the ﬁlters in the calibration instructions.

–Add a four-digit PIN when signing into the instrument for the ﬁrst time using a Connect

proﬁle.

–Add a four-digit PIN when linking a local instrument proﬁle to a Connect proﬁle.

–Select a region for the Connect cloud-based platform.

–A run cannot be started if a block has never been calibrated on the instrument.

–The options after a calibration run is complete.

–The example ﬁles for the desktop software are embedded in the software and do not need to

be downloaded.

•Updated the following items:

–CqExport checkbox is selected as the default.

–Instructions to sign in with facial authentication.

A.0 18 April 2019 New document (v1.0.1).

Important Licensing Information: These products may be covered by one or more Limited Use Label Licenses. By use of these

products, you accept the terms and conditions of all applicable Limited Use Label Licenses.

NOTICE TO PURCHASER: DISCLAIMER OF LICENSE: Purchase of this software product alone does not imply any license under any

process, instrument or other apparatus, system, composition, reagent or kit rights under patent claims owned or otherwise controlled by

Thermo Fisher Scientiﬁc, either expressly, or by estoppel.

Trademarks: All trademarks are the property of Thermo Fisher Scientiﬁc and its subsidiaries unless otherwise speciﬁed. TaqMan is

a registered trademark of Roche Molecular Systems, Inc., used under permission and license. Cy is a registered trademark of GE

Healthcare. Amazon, Alexa, and all related logos are trademarks of Amazon.com, Inc. or its aliates. Windows is a trademark of

Microsoft Corporation. Chrome is a trademark of Google LLC. Pentium is a trademark of Intel Corporation or its subsidiaries in the U.S.

and/or other countries. Macintosh is a trademark of Apple Inc., registered in the U.S. and other countries.

Contents

■CHAPTER 1 Product information ................................................ 14

Network and password security requirements ..................................... 14

Network conﬁguration and security .......................................... 14

Password security ......................................................... 14

Instrument hardware description ................................................. 15

Overview of the instrument .................................................. 15

Features of each instrument ................................................. 16

Instrument ﬁlters and supported dyes ........................................ 16

Overview of data collection ................................................. 18

VeriFlex™Zones ........................................................... 18

AutoDelta settings ......................................................... 19

Parts of the instrument ..................................................... 20

Instrument status indicator .................................................. 22

Hands-free features ............................................................ 22

Facial authentication ....................................................... 22

Voice commands .......................................................... 22

Indicators for the hands-free features ........................................ 23

Software description ........................................................... 24

Parts of the home screen ................................................... 24

Connect and Cloud deﬁnitions .............................................. 26

Instrument, desktop software, and Connect platform features ................... 26

Overview of ﬁle locations and ﬁles ........................................... 27

Components of the ﬁles .................................................... 30

Third-party software ....................................................... 31

Network connection options ................................................ 31

Types of runs .................................................................. 31

Standard curve run ........................................................ 31

Relative standard curve run ................................................. 32

Comparative Ct(DDCt) run .................................................. 32

Genotyping run ............................................................ 33

Presence/absence run ...................................................... 33

Melt curve run ............................................................. 33

QuantStudio™6 Pro Real-Time PCR System and QuantStudio™7 Pro Real-Time PCR System User Guide 5

System template ﬁle names ..................................................... 34

System template ﬁle names for the 96-well 0.2-mL block ....................... 34

System template ﬁle names for the 96-well 0.1-mL block ....................... 35

System template ﬁle names for the 384-well block ............................. 37

System template ﬁle names for the TaqMan™Array Card block .................. 38

Workﬂow ..................................................................... 40

■CHAPTER 2 Get started .......................................................... 41

Precautions for use ............................................................. 41

Installation and instrument veriﬁcation ............................................ 42

Overview of guest access ....................................................... 42

Use the instrument as a guest ............................................... 42

Power on the instrument ........................................................ 43

Enable or disable the microphone ................................................ 44

Use voice commands .......................................................... 45

Sign out ...................................................................... 46

■CHAPTER 3 Create and run plates on the instrument ......................... 47

Options to run a plate .......................................................... 47

Create and run a plate from a system template or a saved plate ﬁle .............. 47

Repeat the last run ......................................................... 49

Overview of customized data export .............................................. 50

(Optional) Scan a barcode using a barcode scanner ................................ 51

Load a plate into the instrument .................................................. 51

Load a TaqMan™Array Card into the instrument ................................... 52

Unload a plate or a TaqMan™Array Card from the instrument ........................ 52

■CHAPTER 4 Edit a plate before starting a run .................................. 54

Overview of a template ﬁle with restricted editing .................................. 54

Options to edit the properties of a plate ﬁle ........................................ 55

Import a sample setup ..................................................... 55

Import an auto export setting ................................................ 55

Delete an auto export setting ................................................ 55

Options to edit the method of a plate ﬁle .......................................... 56

Method elements .......................................................... 57

Edit the method ........................................................... 57

Add or remove steps ....................................................... 58

Add or remove stages ...................................................... 58

Add or remove data collection locations ...................................... 58

Contents

6QuantStudio™6 Pro Real-Time PCR System and QuantStudio™7 Pro Real-Time PCR System User Guide

Set up or remove VeriFlex™Zones ........................................... 59

Set up or remove the Auto Delta feature ...................................... 61

Conﬁgure ramp rates ....................................................... 62

Add or remove a pause ..................................................... 62

Options to edit the well details of a plate ﬁle ....................................... 62

Options to view a plate layout ............................................... 63

Assign or edit a well for a plate .............................................. 65

Assign or edit a well for a TaqMan™Array Card ................................ 66

Add or edit the reagent details for a plate ..................................... 66

Apply the reagents to a plate ................................................ 67

Delete the reagent details ................................................... 67

Add or edit the reagent details for a TaqMan™Array Card ....................... 68

Apply the reagents to a TaqMan™Array Card .................................. 68

Edit a passive reference dye ................................................ 68

Import an Assay Information File (AIF) ........................................ 69

■CHAPTER 5 Options for a run .................................................... 70

Screens available during a run ................................................... 70

Edit a plate ﬁle during a run ..................................................... 71

Pause an instrument run ........................................................ 72

Stop an instrument run ......................................................... 72

View the method during a run ................................................... 73

View real-time data and plots during a run ........................................ 73

Adjust the display of real-time plots during a run ............................... 74

View the time remaining during a run ............................................. 74

Lock the touchscreen during a run ............................................... 74

Unlock the touchscreen during a run ............................................. 75

Instrument Schedule ........................................................... 75

Overview of the instrument schedule ......................................... 75

Schedule a run ............................................................ 75

Cancel a scheduled run .................................................... 75

■CHAPTER 6 View and manage ﬁles ............................................. 77

Manage plate ﬁles .............................................................. 77

Copy plate ﬁles ............................................................ 77

Delete plate ﬁles ........................................................... 78

Manage data ﬁles .............................................................. 78

View QC Check status after a run ............................................ 78

View an ampliﬁcation plot after a run ......................................... 80

Transfer a data ﬁle immediately after a run .................................... 81

Transfer data ﬁles at a later time ............................................. 81

View the list of data ﬁles on the instrument .................................... 82

Delete data ﬁles from the instrument ......................................... 82

Contents

QuantStudio™6 Pro Real-Time PCR System and QuantStudio™7 Pro Real-Time PCR System User Guide 7

■CHAPTER 7 Calibrate and verify instrument performance ..................... 84

Instrument and block calibration ................................................. 84

Calibration and veriﬁcation schedule ............................................. 85

Calibration descriptions ......................................................... 86

View the calibration status and set reminders ...................................... 87

View the calibration status on the instrument .................................. 87

Set calibration frequency and reminders on the instrument ...................... 88

View calibration status and set reminders on the Connect platform .............. 88

Review calibration status ................................................... 89

Export a calibration report ....................................................... 89

Perform ROI/uniformity, background, and dye calibrations for plate blocks ............ 89

Calibration workﬂow ....................................................... 90

Prepare a calibration plate .................................................. 90

Perform calibrations ........................................................ 91

View the calibration images ................................................. 93

Transfer calibration results .................................................. 94

Transfer calibration data ﬁles ................................................ 94

Troubleshoot calibration failure .............................................. 95

Identify contamination ...................................................... 95

Create a background plate (optional) ......................................... 96

Perform ROI/uniformity, background, dye, and normalization calibrations for the

TaqMan™Array Card block .................................................... 97

Calibration workﬂow ....................................................... 97

Prepare a calibration TaqMan™Array Card .................................... 98

Perform calibrations ....................................................... 100

View the calibration images ................................................ 101

Troubleshoot normalization calibration failure ................................ 102

Perform veriﬁcation using RNase P plates ........................................ 103

Instrument veriﬁcation description .......................................... 104

RNase P instrument veriﬁcation plate ....................................... 104

Performance speciﬁcations pass criteria ..................................... 105

Prepare an RNase P plate ................................................. 105

Perform RNase P veriﬁcation ............................................... 106

Troubleshoot veriﬁcation failure ............................................. 107

Perform veriﬁcation using RNase P with a TaqMan™Array Card ..................... 108

RNase P instrument veriﬁcation TaqMan™Array Card ......................... 109

Prepare an RNase P TaqMan™Array Card ................................... 110

Perform RNase P veriﬁcation ............................................... 112

Calibrate custom dyes ......................................................... 113

Overview of custom dyes .................................................. 113

Use a dilution series to determine an optimal custom dye concentration ......... 114

Calibrate the custom dye .................................................. 117

Calibrate for a custom melt curve run ............................................ 120

Contents

8QuantStudio™6 Pro Real-Time PCR System and QuantStudio™7 Pro Real-Time PCR System User Guide

■CHAPTER 8 Manage proﬁles ................................................... 122

Require sign-in ............................................................... 122

Recommended order to set up proﬁles .......................................... 123

Overview of local instrument proﬁles and Connect proﬁles ......................... 123

Connect instrument proﬁle roles and functions ................................... 124

Test the connection to the Connect platform ..................................... 124

Link the instrument to your Connect account ..................................... 126

Create a new local instrument proﬁle ............................................ 127

Link a local proﬁle to a Connect proﬁle .......................................... 127

Unlink a Connect account ...................................................... 129

If you link when you are signed in to the instrument ............................... 129

If you link when you are not signed in to the instrument ............................ 130

Manage individual instrument proﬁles ........................................... 131

Create an administrator instrument proﬁle during initial start-up ................ 131

Set up facial authentication at the initial creation of an instrument proﬁle ........ 131

Add facial authentication to an existing instrument proﬁle ...................... 132

Change the PIN for an instrument proﬁle .................................... 133

Change the PIN for a Connect proﬁle ....................................... 133

Manage all instrument proﬁles as an administrator ................................ 133

View all instrument proﬁles ................................................. 133

Reset the PIN for a proﬁle ................................................. 134

Add a proﬁle ............................................................. 134

Enable or disable administrator privileges .................................... 135

Delete a proﬁle ........................................................... 135

■CHAPTER 9 Use the instrument with the Security, Auditing, and

E‑signature (SAE) v2.0 module ................................................. 136

Overview of the Security, Auditing, and E‑signature (SAE) v2.0 module components ... 137

Overview of the instrument features when the SAE module is enabled ............... 137

Security, Auditing, and E‑signature (SAE) v2.0 module functions .................... 138

Functions that are controlled ............................................... 138

Functions that can be audited ............................................. 139

Functions that can be signed ............................................... 139

Security, Auditing, and E‑signature (SAE) v2.0 module roles ........................ 139

Dialog boxes in the SAE module ................................................ 140

Proﬁles when the SAE module is enabled ........................................ 141

SAE-enabled system components .............................................. 141

Compatibility between SAE-enabled and SAE-disabled components ............ 142

Contents

QuantStudio™6 Pro Real-Time PCR System and QuantStudio™7 Pro Real-Time PCR System User Guide 9

Enable SAE functions ......................................................... 143

Workﬂow: Enable SAE functions ............................................ 143

Conﬁgure SAE Administrator Console application proﬁles ..................... 143

Enable SAE on the instrument and specify the SAE server (administrator only) ... 143

Connect to the SAE server ................................................. 144

Enable SAE functions in QuantStudio™Design and Analysis Software v2 ........ 145

Disable SAE on the instrument (administrator only) ................................ 145

Sign out with SAE enabled ..................................................... 148

Change your SAE account password on the instrument ............................ 149

Sign a plate setup ............................................................. 150

Enter an audit reason .......................................................... 151

View signing records for a plate ﬁle .............................................. 152

View audit records ............................................................ 153

Use the instrument when the SAE server is oine ................................. 154

E-signature requirements to start a run .......................................... 154

Signing in after automatic screen locking ........................................ 155

SAE error messages and actions ................................................ 155

■CHAPTER 10 Maintain the instrument ......................................... 156

Install a block ................................................................ 156

Change the block ............................................................. 157

Remove the block ............................................................. 158

Decontaminate the sample block ............................................... 159

Materials required ........................................................ 159

Clean the sample block ................................................... 159

Detailed procedures for cleaning the sample block ............................ 160

Replace the instrument fuses ................................................... 161

Materials required ........................................................ 161

Replace the fuses ........................................................ 161

Power on or o, store, and move ................................................ 163

Enable and edit sleep mode ............................................... 163

Power on the instrument ................................................... 164

Power o the instrument ................................................... 164

Prepare the instrument to store, move, or ship ............................... 165

Move the instrument ...................................................... 165

■CHAPTER 11 Conﬁgure the instrument settings .............................. 166

View the instrument details ..................................................... 166

View the license agreement .................................................... 167

View the privacy policy for the Connect cloud-based platform ...................... 167

Contents

10 QuantStudio™6 Pro Real-Time PCR System and QuantStudio™7 Pro Real-Time PCR System User Guide

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